Contacts of the strand formed by residues 105 - 116 (chain A) in PDB entry 2YD7
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 GLY 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 4.6 2.9 - - - -
24A PRO* 3.4 12.6 - - - +
101A SER* 3.4 0.7 - - - -
102A ASN* 3.0 34.9 + - - +
103A ASN 3.6 0.2 - - - -
104A VAL* 1.3 80.8 - - - +
106A GLU* 1.3 64.4 + - - +
95B ILE* 4.3 9.4 - - - +
110B SER* 3.3 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 5.5 0.2 - - - +
24A PRO* 4.0 2.1 - - - +
99A VAL* 3.7 26.3 - - + +
100A ALA 3.3 13.2 - - - +
101A SER* 3.7 15.0 - - - -
105A GLY* 1.3 75.5 - - - +
107A ILE* 1.3 68.5 + - - +
61B GLY* 5.3 6.3 - - - -
95B ILE* 5.6 0.9 - - + -
97B GLU* 3.8 35.8 - - + +
108B SER* 4.6 6.9 + - - +
109B VAL 3.6 2.6 + - - -
110B SER* 2.9 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 6.0 1.6 - - + -
24A PRO* 3.4 39.7 - - + +
25A ARG* 3.6 2.2 - - - +
26A PHE* 3.6 49.8 - - + +
99A VAL* 3.4 3.1 - - - +
100A ALA* 2.8 41.9 + - + +
106A GLU* 1.3 82.2 - - - +
108A SER* 1.3 62.7 + - - +
108B SER* 3.3 15.9 - - - +
109B VAL* 4.3 15.5 - - + -
110B SER* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.8 7.2 - - - -
97A GLU* 5.2 6.6 - - - +
98A CYS 3.1 14.4 - - - -
99A VAL* 3.9 19.1 - - - -
107A ILE* 1.3 75.8 - - - +
109A VAL* 1.3 63.9 + - - +
99B VAL* 5.7 0.7 - - - +
106B GLU* 5.0 3.6 + - - +
107B ILE* 3.4 8.2 + - - +
108B SER* 2.5 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.8 24.2 - - + -
29A THR* 4.1 15.0 - - + -
30A PRO* 3.8 29.6 - - + +
97A GLU* 3.5 3.7 - - - -
98A CYS* 2.9 30.1 + - + +
108A SER* 1.3 75.9 - - - +
110A SER* 1.3 76.8 + - - +
106B GLU 3.6 7.4 - - - -
107B ILE* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 4.5 8.3 - - - +
32A ASP* 5.0 0.5 - - - +
95A ILE* 3.7 14.3 - - - +
96A TYR 3.2 12.8 - - - -
97A GLU* 4.0 7.6 - - - -
109A VAL* 1.3 87.0 - - - +
111A THR* 1.3 64.6 + - - +
23B PRO* 5.0 7.1 - - - +
104B VAL 4.5 0.9 + - - -
105B GLY* 3.2 10.4 - - - -
106B GLU 2.8 36.2 + - - -
107B ILE* 5.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 3.9 22.4 - - + -
31A VAL* 3.2 9.0 + - - -
32A ASP* 3.1 31.1 + - - -
43A PHE* 3.5 28.1 - - + -
57A TRP* 4.8 2.7 - - + -
95A ILE* 3.4 5.0 - - - +
96A TYR* 2.8 49.3 + - + +
97A GLU 6.2 0.2 - - - -
110A SER* 1.3 77.4 - - - +
112A ARG* 1.3 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP* 2.8 33.9 + - + +
33A GLN 3.0 26.2 + - - +
43A PHE* 3.9 3.4 - - - -
94A ALA 3.8 2.0 - - - -
95A ILE* 4.3 6.5 - - + -
111A THR* 1.3 76.9 + - - +
113A LEU* 1.3 59.9 + - - +
114A THR* 5.1 2.6 + - - +
1221A PO4 2.6 37.7 + - - +
21B GLU* 5.1 6.5 + - - +
103B ASN 5.7 0.4 + - - -
104B VAL* 3.4 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 3.4 13.7 - - + +
35A GLY 4.6 1.8 - - - +
41A ALA* 3.6 26.9 - - + -
43A PHE* 3.7 11.2 - - + -
84A ILE* 3.5 29.8 - - + -
87A LEU* 3.9 13.0 - - + -
92A ASP* 3.6 25.1 - - + +
93A GLU* 3.3 7.1 - - - +
94A ALA 3.0 18.7 + - - -
96A TYR* 3.8 13.6 - - + -
111A THR 4.2 0.4 + - - -
112A ARG* 1.3 72.3 - - - +
114A THR* 1.3 71.8 + - - +
115A VAL* 3.8 9.6 - - + -
1221A PO4 2.7 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 2.9 6.8 + - - +
34A THR* 3.2 30.5 + - + +
35A GLY 2.8 25.0 + - - -
93A GLU* 3.6 15.3 - - - +
112A ARG* 5.1 3.5 + - - +
113A LEU* 1.3 76.4 - - - +
115A VAL* 1.3 66.1 + - - +
116A LEU* 4.2 13.9 - - + -
1221A PO4 3.6 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 3.5 2.7 - - - +
36A VAL 4.1 1.1 - - - -
37A SER* 3.7 21.1 - - - +
87A LEU* 3.9 24.5 - - + -
88A ARG 3.8 18.6 - - - +
89A THR* 2.9 41.9 + - - -
92A ASP* 4.2 2.0 - - + -
93A GLU* 3.4 24.1 + - + +
113A LEU* 3.8 25.4 - - + -
114A THR* 1.3 82.1 - - - +
116A LEU* 1.3 64.0 + - - +
117A ARG 4.0 0.2 + - - -
120A GLN* 4.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.6 25.6 - - + -
35A GLY 2.9 11.3 + - - +
36A VAL* 3.5 3.1 - - - -
37A SER* 2.7 31.0 + - - -
89A THR* 4.4 2.5 - - - -
114A THR* 4.3 14.8 - - + -
115A VAL* 1.3 76.3 - - - +
117A ARG* 1.3 66.3 + - - +
120A GLN* 4.0 25.8 - - + +
121A ILE* 4.2 7.2 - - + -
122A PRO* 3.6 31.6 - - + -
125A PHE* 4.1 13.0 - - + -
207A ALA 4.3 2.7 - - - +
----------------------------------------------------------
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