Contacts of the strand formed by residues 85 - 103 (chain B) in PDB entry 4V1M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 85 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN 3.6 3.6 - - - -
74B LEU* 3.6 30.9 - - - +
75B ALA 4.0 2.8 + - - -
83B ASN 4.3 0.2 - - - -
84B ILE* 1.3 73.9 + - - +
86B ARG* 1.3 59.7 + - - +
87B LYS* 5.8 0.2 - - - -
138B GLU* 3.2 2.6 - - - +
139B ALA* 2.6 54.4 + - - +
140B ILE 5.7 0.2 - - - -
141B ASP* 4.6 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 4.9 0.2 - - - -
72B GLU* 3.2 1.6 - - - +
73B GLN* 2.8 40.2 + - + +
74B LEU* 3.7 2.1 - - - +
84B ILE* 3.8 18.3 - - + +
85B SER* 1.3 77.4 - - - +
87B LYS* 1.3 69.3 + - - +
88B TYR* 3.3 41.9 + - + +
136B THR* 4.7 9.3 - - - +
137B TYR 3.2 10.5 - - - +
138B GLU* 2.9 39.2 + - + +
151B LEU* 5.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 5.1 14.8 - - + +
71B LEU 3.7 6.1 - - - +
72B GLU* 3.5 35.5 + - + +
74B LEU* 4.6 7.0 - - + -
86B ARG* 1.3 79.9 - - - +
88B TYR* 1.3 62.5 + - - +
89B GLU* 5.6 1.1 - - + -
137B TYR* 2.8 53.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU 4.2 0.2 - - - +
70B ILE* 3.2 8.5 - - - +
71B LEU* 2.9 56.1 + - + +
73B GLN* 4.3 17.8 - - + +
86B ARG* 3.3 41.1 + - + +
87B LYS* 1.3 72.8 - - - +
89B GLU* 1.3 64.6 + - - +
90B ILE* 6.5 0.4 - - + -
134B LYS* 5.8 3.8 - - + -
135B ARG 3.6 6.5 - - - +
136B THR* 3.5 35.0 - - + +
432B MET* 5.7 5.3 - - - +
436B VAL* 3.6 32.3 - - + +
442B PHE* 5.6 14.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 5.4 6.0 - - - +
69B LEU 4.0 0.2 - - - -
70B ILE* 3.5 23.3 - - + +
87B LYS* 5.6 0.7 - - + -
88B TYR* 1.3 75.9 - - - +
90B ILE* 1.3 71.6 + - - +
91B SER* 3.6 16.5 + - - +
133B LYS 4.3 0.2 - - - -
134B LYS* 3.3 6.4 - - - +
135B ARG* 2.9 42.2 + - + +
137B TYR* 3.5 35.0 + - + -
432B MET* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 3.2 7.0 - - - -
69B LEU* 3.2 42.0 + - + +
70B ILE* 4.9 0.4 - - - +
88B TYR* 6.5 0.2 - - + -
89B GLU* 1.3 80.7 - - - +
91B SER* 1.3 62.7 + - - +
92B PHE* 4.2 19.6 - - + -
132B VAL* 4.1 16.8 - - + -
133B LYS 3.3 3.4 - - - -
134B LYS* 3.6 34.1 - - + +
428B ILE* 4.3 13.5 - - + -
432B MET* 3.4 33.0 - - + -
444B MET* 5.1 7.0 - - + -
447B ALA* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 3.6 17.2 - - - +
89B GLU* 3.6 19.8 + - - +
90B ILE* 1.3 76.9 + - - +
92B PHE* 1.3 64.1 + - - +
93B GLY 4.1 0.2 - - - -
131B ASP 3.6 0.3 - - - +
132B VAL* 3.3 10.9 - - - +
133B LYS* 2.8 48.3 + - - +
135B ARG* 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.1 17.1 - - + +
64B CYS* 4.4 13.9 - - - -
67B SER* 3.6 36.0 - - - -
68B THR* 4.2 6.6 - - - +
69B LEU* 3.9 13.2 - - + -
90B ILE* 4.2 11.9 - - + -
91B SER* 1.3 78.2 - - - +
93B GLY* 1.3 62.7 + - - +
130B VAL* 3.7 24.5 - - + -
131B ASP 3.5 0.9 - - - -
132B VAL* 3.7 25.8 - - + -
167B ILE* 6.0 4.7 - - + -
421B PHE* 4.1 24.9 - + - -
424B LEU* 6.1 1.6 - - + -
425B THR* 4.5 2.5 - - - -
428B ILE* 4.1 25.1 - - + -
448B ILE* 5.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 3.2 18.2 + - - -
63B ILE* 3.7 5.5 - - - +
64B CYS* 5.4 1.1 - - - -
91B SER 4.1 0.8 - - - -
92B PHE* 1.3 75.2 - - - +
94B LYS* 1.3 69.9 + - - +
130B VAL* 4.2 1.8 - - - +
131B ASP* 2.8 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 3.6 11.4 - - - +
93B GLY* 1.3 72.9 - - - +
95B ILE* 1.3 72.4 - - - +
96B TYR* 3.9 28.3 + - + +
130B VAL* 3.6 2.3 - - - -
131B ASP* 3.1 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL 5.9 1.1 - - - +
59B LEU* 3.7 40.2 - - + +
60B GLN* 3.0 44.3 + - + +
63B ILE* 4.4 14.8 - - + -
94B LYS* 1.3 83.2 - - - +
96B TYR* 1.3 72.3 + - - +
97B VAL* 5.4 2.0 - - + +
128B LEU* 4.1 14.4 - - + -
129B PHE 3.4 10.5 - - - +
130B VAL* 3.7 18.8 - - + -
167B ILE* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.9 28.3 + - + +
95B ILE* 1.3 82.8 - - - +
97B VAL* 1.3 66.2 + - - +
98B THR* 6.4 1.1 - - + -
127B GLY 4.4 0.2 - - - -
128B LEU* 3.7 3.3 - - - -
129B PHE* 2.5 52.2 + - + +
131B ASP* 3.4 37.3 + - - -
164B LYS* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.1 22.0 - - + +
59B LEU* 5.2 4.5 - - + -
95B ILE* 5.4 2.5 - - + +
96B TYR* 1.3 81.1 - - - +
98B THR* 1.3 68.9 + - - +
126B SER* 3.5 21.5 - - - +
127B GLY 3.2 8.7 - - - +
128B LEU* 3.8 17.7 - - + -
170B LEU* 4.8 7.4 - - + -
172B ILE* 5.0 0.9 - - + -
178B ASN* 3.9 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 6.4 0.9 - - + -
97B VAL* 1.3 73.1 - - - +
99B LYS* 1.3 65.0 + - - +
101B MET* 3.3 21.4 - - + +
126B SER* 3.1 9.4 - - - -
127B GLY* 3.0 30.8 + - - -
129B PHE* 4.2 20.9 - - + -
178B ASN* 2.6 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B THR* 1.3 90.5 + - - +
100B PRO* 1.3 70.2 - - - +
101B MET* 3.4 8.0 - - + +
126B SER* 3.5 2.1 - - - -
177B LYS 4.0 6.1 + - - -
178B ASN* 3.3 23.3 + - - +
179B CYS 3.4 15.8 + - - -
180B TYR* 3.4 38.9 - - + +
183B GLU* 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LYS* 1.3 86.7 - - + +
101B MET* 1.3 59.8 + - - +
111B ALA* 3.7 0.2 - - - -
112B LEU* 3.5 10.7 + - + +
124B TYR* 3.6 44.4 - - + +
125B SER 3.3 15.9 - - - +
126B SER* 3.6 2.5 - - - -
172B ILE* 3.8 19.5 - - + -
178B ASN* 3.4 22.4 - - - +
180B TYR* 2.5 36.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B THR* 3.3 37.5 - - + +
99B LYS 3.4 6.7 + - - +
100B PRO* 1.3 77.7 - - - +
102B VAL* 1.3 70.2 + - - +
109B THR* 3.9 19.3 - - + -
110B HIS* 3.5 17.7 - - - +
111B ALA* 4.7 2.2 - - - +
112B LEU* 4.0 9.7 - - - +
123B THR 4.7 0.7 - - - +
125B SER* 3.2 9.4 + - - +
126B SER* 4.4 0.4 - - - +
127B GLY* 5.0 3.8 - - - +
129B PHE* 5.3 8.5 - - + -
166B PHE* 6.5 0.4 - - + -
169B ARG* 3.4 36.7 + - - +
180B TYR* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B MET* 1.3 81.2 - - - +
103B ASN* 1.3 61.0 + - - +
104B GLU* 3.6 19.7 + - + +
109B THR* 3.3 25.9 - - - +
110B HIS* 3.0 33.2 + - + +
112B LEU* 3.6 29.4 - - + -
120B ARG* 4.9 1.8 - - - +
122B LEU* 3.9 24.0 - - + -
123B THR 4.7 3.6 - - - +
169B ARG* 4.5 2.0 - - - +
958B GLN* 3.8 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 1.3 73.3 - - - +
104B GLU* 1.3 73.6 + - - +
107B GLY* 3.2 25.3 + - - -
108B VAL 4.1 1.1 - - - -
109B THR* 3.0 21.0 + - + +
169B ARG* 4.8 15.4 + - - +
958B GLN* 3.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il