Contacts of the strand formed by residues 112 - 124 (chain A) in PDB entry 4IHB
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 PRO 112 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 5.3 1.8 - - + -
105A LEU 3.6 9.0 - - - +
106A LEU* 3.9 5.6 - - + -
107A ASP* 4.6 3.5 - - - +
110A LYS 4.7 0.4 - - - +
111A GLN* 1.3 91.2 - - + +
113A THR* 1.3 60.6 + - - +
114A GLY 4.3 2.7 - - - +
0C PHE* 3.0 33.7 - - + -
59C LEU* 5.0 0.2 - - + -
92C LEU* 3.6 31.2 - - + -
97C LEU* 3.5 34.3 - - + -
123C TYR* 4.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN 5.4 0.9 - - - +
81A LEU 3.5 23.9 + - - +
82A GLY* 4.2 0.7 - - - -
105A LEU* 2.9 29.3 + - - +
106A LEU 3.8 2.5 - - - +
107A ASP* 3.7 27.8 - - + +
112A PRO* 1.3 73.2 - - - +
114A GLY* 1.3 57.2 + - - +
115A ALA* 3.1 25.8 + - - +
0C PHE* 5.0 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 3.7 19.4 - - - +
105A LEU 4.5 0.2 + - - -
112A PRO* 3.4 5.7 - - - +
113A THR* 1.3 78.6 - - - +
115A ALA* 1.3 62.3 + - - +
116A SER* 5.3 1.6 + - - -
0C PHE* 5.0 4.4 - - - -
95C PRO 5.7 0.9 - - - +
97C LEU* 5.2 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.3 10.5 - - - +
11A ASN 3.3 20.4 + - - +
12A VAL* 4.2 11.2 - - + -
13A HIS 5.3 0.7 - - - +
104A PRO* 3.5 5.5 - - - +
105A LEU* 2.9 39.0 + - + +
113A THR* 3.1 16.5 + - - +
114A GLY* 1.3 83.3 + - - +
116A SER* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.1 8.0 - - - +
10A GLU* 3.0 44.9 + - - +
102A ASN* 3.9 17.8 + - - -
103A ALA 3.4 12.3 - - - -
104A PRO* 4.3 1.8 - - - -
105A LEU* 4.2 4.3 - - - +
114A GLY 5.3 1.0 + - - -
115A ALA* 1.3 75.9 - - - +
117A LEU* 1.3 61.3 + - - +
118A VAL* 5.5 0.6 - - - +
205A FMT 4.2 5.2 + - - -
95C PRO* 4.1 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.0 15.3 - - + -
8A TYR 3.3 18.2 - - - +
9A ALA* 4.1 3.1 - - + -
24A CYS* 4.0 13.2 - - - -
46A TRP* 3.7 24.5 - - + -
67A VAL* 3.6 38.1 - - + -
69A VAL* 4.6 3.6 - - + -
84A ALA* 5.7 0.2 - - + -
102A ASN* 3.6 0.9 - - - -
103A ALA* 2.7 41.6 + - + +
105A LEU* 4.1 18.8 - - + -
116A SER* 1.3 74.9 - - - +
118A VAL* 1.3 62.9 + - - +
119A LEU* 3.6 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.0 0.9 - - - -
7A LEU* 3.0 38.2 + - + -
8A TYR* 2.8 55.3 + - + +
10A GLU* 5.9 0.4 - - + -
100A SER* 6.5 0.4 - - - -
101A PHE 3.4 7.0 - - - +
102A ASN* 3.3 20.2 - - + +
116A SER* 5.5 1.1 - - - +
117A LEU* 1.3 72.7 - - - +
119A LEU* 1.3 66.0 + - - +
205A FMT 3.2 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.4 5.2 - - + -
5A PHE 3.1 14.1 - - - +
6A ILE* 4.3 9.9 - - + -
7A LEU* 4.4 2.9 - - - +
65A LEU* 3.8 29.2 - - + -
67A VAL* 4.4 9.4 - - + -
86A VAL* 4.3 19.5 - - + -
100A SER* 3.6 3.8 - - - -
101A PHE* 2.9 51.3 + - + +
103A ALA* 4.9 3.4 - - + -
117A LEU* 3.6 35.4 - - + +
118A VAL* 1.3 78.2 - - - +
120A GLN* 1.3 61.6 + - - +
121A VAL* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG 3.9 0.3 - - - +
4A VAL* 3.3 4.5 - - - +
5A PHE* 2.7 64.5 + - + +
7A LEU* 5.0 8.3 - - + +
98A SER* 3.7 9.1 - - - -
99A ALA 3.4 8.5 - - - +
100A SER* 3.6 12.2 - - - -
119A LEU* 1.3 74.7 - - - +
121A VAL* 1.3 83.6 + - - +
122A SER* 4.5 4.6 - - - -
202A FMT 2.7 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.5 27.8 - - + -
3A ARG 3.4 5.6 - - - +
4A VAL* 3.9 16.2 - - + -
65A LEU* 4.2 5.8 - - + -
88A LEU* 3.9 17.0 - - + -
91A VAL* 4.1 7.7 - - + +
98A SER* 3.2 3.6 - - - -
99A ALA 2.9 35.4 + - - +
101A PHE* 3.8 27.6 - - + -
119A LEU* 4.2 14.1 - - + -
120A GLN* 1.3 84.3 + - - +
122A SER* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 3.7 0.9 - - - +
2A LEU* 3.5 6.1 - - - +
3A ARG* 2.7 81.7 + - - +
5A PHE* 5.5 2.9 - - - -
91A VAL* 4.9 0.7 - - - -
97A LEU 3.7 8.0 + - - -
98A SER* 4.3 10.5 - - - -
120A GLN* 4.5 5.4 - - - -
121A VAL* 1.3 76.8 - - - +
123A TYR* 1.3 61.5 + - - +
124A THR* 3.8 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A PHE 4.1 15.4 + - - -
1A MET 3.6 10.8 - - - -
2A LEU* 4.7 2.2 - - + -
54A LEU* 3.5 24.2 - - + -
58A PRO* 3.3 16.5 - - - +
59A LEU* 3.1 48.1 + - + -
91A VAL* 3.7 11.6 - - + +
92A LEU* 3.7 25.4 - - + -
97A LEU* 2.9 41.6 + - + +
122A SER* 1.3 71.8 + - - +
124A THR* 1.3 60.8 + - - +
110B LYS 4.2 1.6 + - - -
111B GLN* 4.7 0.5 - - - +
112B PRO* 3.5 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A PHE 3.5 5.0 + - - -
1A MET* 2.8 55.7 + - + +
3A ARG* 3.8 35.6 + - + +
51A GLU* 5.7 0.2 - - - +
122A SER* 3.8 10.1 + - - +
123A TYR* 1.3 75.7 - - - +
125A ALA* 1.3 73.9 + - - +
----------------------------------------------------------
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