Contacts of the strand formed by residues 97 - 106 (chain A) in PDB entry 4HH3
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 GLU 97 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.6 26.0 - - + +
89A ASN* 4.9 8.8 - - + +
90A HIS 3.2 15.5 - - - +
91A ILE* 4.3 11.5 - - + +
95A SER 3.7 4.6 + - - +
96A PHE* 1.3 79.3 - - - +
98A PHE* 1.3 62.1 + - - +
99A PRO* 4.5 1.4 - - - +
128A GLN* 5.4 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 5.0 2.7 - - + -
47A PHE* 3.7 30.3 - + + -
50A LEU* 4.5 9.0 - - + -
53A TRP* 3.8 26.0 - + - -
88A LEU 4.0 0.2 - - - +
89A ASN* 4.5 3.1 - - - -
90A HIS* 2.8 53.2 + + + +
92A ASP* 4.0 30.7 - - + -
96A PHE* 4.5 3.8 - - + -
97A GLU* 1.3 75.9 - - - +
99A PRO* 1.3 67.5 - - + +
100A ILE* 3.7 32.9 + - + -
121A ARG* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 4.8 7.2 - - + -
88A LEU 3.4 7.2 - - - +
89A ASN* 3.6 18.4 - - - +
97A GLU 4.5 1.1 - - - +
98A PHE* 1.3 90.0 - - + +
100A ILE* 1.3 68.5 + - - +
120A LEU* 3.1 45.8 + - + -
121A ARG* 3.9 7.5 + - - +
124A ALA* 3.9 30.1 - - + -
127A GLN* 6.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.9 11.0 - - + -
47A PHE* 3.8 25.1 - - + -
86A VAL 3.5 0.9 - - - +
87A GLU* 3.6 0.9 - - - -
88A LEU* 2.9 30.5 + - - +
90A HIS* 3.9 10.3 - - + -
98A PHE* 3.7 17.7 - - + -
99A PRO* 1.3 83.9 - - - +
101A ARG* 1.3 62.3 + - - +
102A TYR* 3.4 36.6 + - + +
117A GLY* 3.6 20.2 - - - -
118A ARG 3.4 9.4 - - - +
119A ASP* 3.8 20.6 - - - +
120A LEU* 4.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 3.8 28.3 - - + -
86A VAL 3.4 10.8 - - - +
87A GLU* 4.3 5.6 - - + +
100A ILE* 1.3 72.4 - - - +
102A TYR* 1.3 59.7 - - - +
103A ILE* 5.8 0.6 - - + +
116A LEU 3.8 1.4 - - - +
117A GLY* 3.5 0.9 - - - -
118A ARG* 2.9 76.4 + - + +
120A LEU* 3.7 35.8 - - + +
123A ILE* 5.9 1.0 - - - +
122B PRO* 5.8 6.5 - - - +
123B ILE* 6.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.3 12.1 - - + +
27A LEU* 3.8 15.8 - - + +
85A ALA* 3.3 4.3 - - - -
86A VAL* 2.7 46.4 + - + +
88A LEU* 3.7 22.9 - - + -
90A HIS* 2.7 36.8 + + - -
100A ILE* 3.4 34.4 - - + +
101A ARG* 1.3 73.2 - - - +
103A ILE* 1.3 62.9 + - - +
104A LEU* 4.1 15.7 - - + -
115A MET* 3.5 47.6 - - + -
116A LEU 3.3 3.1 - - - -
117A GLY* 3.6 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 4.1 4.0 - - - -
83A SER* 3.7 22.2 - - - +
85A ALA* 3.7 34.5 - - + +
101A ARG* 5.8 0.4 - - - +
102A TYR* 1.3 74.3 - - - +
104A LEU* 1.3 63.2 + - - +
105A HIS* 3.5 27.0 - - + +
114A LEU 3.6 2.3 - - - +
115A MET* 3.6 0.7 - - - -
116A LEU* 3.0 38.5 + - + +
118A ARG* 4.4 11.7 - - - +
21B THR* 4.3 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 4.3 22.0 - - + +
73A ARG* 4.0 37.0 - - + +
74A SER* 4.3 7.0 - - - -
77A LEU* 3.7 16.1 - - + +
82A GLY* 3.3 4.9 - - - -
83A SER* 2.8 38.1 + - - +
86A VAL* 4.2 10.1 - - + -
88A LEU* 5.1 1.6 - - + -
102A TYR* 4.1 9.0 - - + -
103A ILE* 1.3 76.7 - - - +
105A HIS* 1.3 61.7 + - - +
113A ILE* 4.0 5.2 - - + -
114A LEU 3.6 2.7 - - - -
115A MET* 3.8 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.0 3.6 - - - -
81A ARG* 4.6 3.4 - - - -
82A GLY* 3.7 21.9 + - - -
103A ILE* 3.5 16.1 - - + +
104A LEU* 1.3 79.4 - - - +
106A ARG* 1.3 62.3 + - - +
107A LEU* 3.6 9.6 + - + +
113A ILE* 3.3 4.4 - - - -
114A LEU* 2.9 36.3 + - + +
116A LEU* 3.7 15.6 - - + +
14B LEU* 4.7 7.4 - - + +
17B ASP* 3.7 23.5 + - + -
18B LEU* 3.3 32.3 - - + +
21B THR* 3.0 29.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 4.3 16.4 + - - +
74A SER* 2.7 31.3 + - - -
75A GLU* 4.6 5.3 + - - +
77A LEU* 2.9 39.7 + - + +
78A GLU 3.8 12.3 + - - -
79A PRO* 3.5 36.6 - - + +
80A GLY 4.8 0.9 + - - -
81A ARG 5.4 1.0 + - - -
105A HIS* 1.3 71.1 - - - +
107A LEU* 1.3 64.6 + - - +
108A PRO* 3.7 2.1 - - - +
111A ARG* 2.8 64.8 + - + +
112A SER 3.6 2.9 - - - -
113A ILE* 3.8 22.9 - - - +
14B LEU* 5.3 2.9 - - - +
----------------------------------------------------------
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