Contacts of the helix formed by residues 87 - 105 (chain A) in PDB entry 4D1Q
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 1.3 76.1 - - - +
88A ALA* 1.3 56.2 + - - +
89A ASP* 2.9 10.4 + - - +
90A CYS* 2.7 36.9 + - - +
91A LYS* 2.8 12.6 + - - +
130B GLU* 5.4 0.5 + - - -
131B TYR* 2.6 25.3 + - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL 3.5 2.2 + - - -
87A SER* 1.3 70.9 - - - +
89A ASP* 1.3 59.3 + - - +
91A LYS* 3.9 12.2 - - + +
92A LYS* 3.2 30.0 + - - +
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 2.9 9.6 - - - +
88A ALA* 1.3 79.5 - - - +
90A CYS* 1.3 64.1 + - - +
92A LYS* 3.6 7.7 - - - +
93A GLU* 3.4 16.8 + - - +
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Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.6 22.0 - - + -
87A SER* 2.7 23.5 + - - +
89A ASP* 1.3 74.4 - - - +
91A LYS* 1.3 55.8 + - - +
92A LYS 3.0 1.3 - - - -
93A GLU* 2.6 30.6 + - - +
94A ALA 2.8 9.9 + - - -
123B PHE* 3.9 3.7 - - - -
126B LYS* 6.1 3.4 - - - +
127B VAL* 4.0 31.0 - - - -
130B GLU* 5.5 1.3 - - - +
131B TYR* 3.8 17.3 - - + +
140B LEU* 4.6 6.5 - - - -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 4.0 12.3 - - + +
87A SER 2.8 14.1 + - - +
88A ALA* 4.0 11.2 - - - +
90A CYS* 1.3 76.2 - - - +
92A LYS* 1.3 60.2 + - - +
94A ALA* 3.1 20.9 - - - +
95A ILE* 3.2 15.4 + - + +
139B GLU* 2.6 46.2 + - - +
140B LEU* 3.1 29.2 - - + +
142B PRO* 4.8 6.1 - - + -
5D T 4.7 9.4 + - - +
6D G 3.5 20.4 + - - -
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA 3.2 20.9 + - - +
89A ASP* 3.6 12.1 - - - +
90A CYS 3.0 0.4 - - - -
91A LYS* 1.3 75.4 - - - +
93A GLU* 1.3 64.1 + - - +
94A ALA 3.3 0.3 + - - -
95A ILE* 3.5 14.3 + - + +
96A GLU* 3.4 34.4 + - + +
150B LYS* 6.2 3.1 - - - -
4D T 5.3 1.2 + - - -
5D T 3.8 22.7 - - - +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASP 3.4 9.2 + - - +
90A CYS* 2.6 14.5 + - - +
92A LYS* 1.3 74.2 - - - +
94A ALA* 1.3 62.2 + - - +
96A GLU* 3.6 15.9 + - + +
97A LYS* 3.1 46.9 + - + +
123B PHE* 3.1 32.4 - - + -
126B LYS* 3.6 23.3 + - - +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A CYS 2.8 10.1 + - - +
91A LYS* 3.1 13.2 - - - +
93A GLU* 1.3 76.5 - - - +
95A ILE* 1.3 70.3 + - - +
97A LYS* 3.2 1.7 + - - +
98A CYS* 3.0 24.7 + - - -
123B PHE* 3.2 22.3 - - + -
124B PHE* 4.8 4.4 - - + -
140B LEU* 3.9 32.3 - - + +
142B PRO* 4.8 5.2 - - + -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 3.2 16.3 + - + +
92A LYS* 3.5 17.3 - - + +
94A ALA* 1.3 80.6 - - - +
96A GLU* 1.3 69.5 + - - +
98A CYS* 2.7 11.0 + - - +
99A ALA* 3.1 9.6 + - + -
142B PRO* 3.9 29.3 - - + +
146B THR* 3.9 20.4 - - + +
147B LEU* 4.2 3.3 - - + +
150B LYS* 3.3 37.0 - - + -
5D T 3.8 32.8 - - - +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 3.4 27.9 + - + +
93A GLU* 3.8 19.1 - - + +
95A ILE* 1.3 82.3 - - + +
97A LYS* 1.3 68.4 + - + +
99A ALA* 3.3 1.7 + - - +
100A GLN* 3.1 41.0 + - - +
150B LYS* 4.1 29.2 + - + +
154B ASP* 5.8 0.7 - - - +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 3.1 34.0 + - + +
94A ALA 3.7 3.1 - - - +
95A ILE 2.9 1.6 + - - -
96A GLU* 1.3 80.6 + - + +
98A CYS* 1.3 61.6 + - - +
100A GLN* 3.7 20.1 + - - +
101A TRP* 3.3 17.2 + - - +
116B GLY 4.8 1.2 - - - +
119B ASP* 3.6 28.7 - - - +
120B MET* 4.0 16.9 - - + +
123B PHE* 3.3 45.5 - - + -
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Residues in contact with CYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 3.0 14.6 + - - +
95A ILE 2.7 13.4 + - - +
97A LYS* 1.3 70.3 - - - +
99A ALA* 1.3 65.8 + - - +
101A TRP* 2.9 22.2 + - - +
102A VAL* 3.0 8.7 + - - +
112A VAL* 4.2 14.4 - - + -
120B MET* 2.8 33.4 - - + -
124B PHE* 4.4 14.8 - - - -
141B LEU* 4.5 2.5 - - - -
142B PRO* 4.4 15.9 - - + -
147B LEU* 3.6 16.8 - - + -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE 3.1 5.5 + - - +
96A GLU 3.6 7.6 - - - +
98A CYS* 1.3 75.8 - - - +
100A GLN* 1.3 59.3 + - + +
102A VAL* 2.8 12.6 + - - +
103A VAL* 2.8 31.4 + - + +
147B LEU* 3.3 17.8 - - + +
150B LYS* 3.9 29.6 - - + -
151B VAL* 4.2 14.6 - - + -
154B ASP* 5.4 2.9 - - - +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.1 32.8 + - - +
97A LYS* 3.7 24.4 + - - +
99A ALA* 1.3 79.5 - - + +
101A TRP* 1.3 54.3 + - - +
103A VAL* 4.2 7.2 - - + -
104A ARG* 2.6 52.7 + - - +
116B GLY* 5.1 1.3 - - - +
154B ASP* 4.3 8.2 + - - +
158B LYS* 5.4 4.6 - - - +
604B TYR* 3.4 40.1 + - + +
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Residues in contact with TRP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LYS 3.3 8.8 + - - +
98A CYS* 2.9 18.9 + - - +
100A GLN* 1.3 79.4 - - - +
102A VAL* 1.3 64.7 + - + +
105A ASP* 2.7 62.8 + - + +
107A ARG* 3.9 19.9 - - + +
111A ALA* 3.7 30.3 - - + -
112A VAL* 3.9 12.8 - - + -
117A PHE* 3.6 37.2 - + - -
101B TRP* 3.8 26.0 - + - -
107B ARG* 5.9 0.9 - - - -
111B ALA 4.9 1.4 + - - -
116B GLY* 4.2 13.9 + - - +
117B PHE* 3.5 27.4 - + - +
120B MET* 3.4 19.5 - - + -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A CYS 3.0 8.2 + - - +
99A ALA* 2.8 15.2 + - - +
101A TRP* 1.3 87.5 - - + +
103A VAL* 1.3 60.3 + - + +
106A CYS* 3.1 8.7 + - - -
107A ARG* 3.1 45.7 + - + +
108A PRO 3.8 22.2 - - - +
109A PHE* 3.5 37.5 - - + +
147B LEU* 4.6 10.5 - - + -
151B VAL* 4.9 1.6 - - + -
597B LEU* 4.1 10.9 - - + +
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA* 2.8 19.8 + - + +
100A GLN* 3.7 6.7 - - - +
102A VAL* 1.3 79.9 - - - +
104A ARG* 1.3 68.3 + - - +
105A ASP 3.3 0.5 + - - -
106A CYS* 3.4 9.9 + - - +
151B VAL* 3.7 29.4 - - + -
597B LEU* 4.1 18.8 - - + +
600B LEU* 3.5 17.9 - - + -
601B ASN* 3.3 48.7 + - + +
604B TYR* 4.2 11.4 - - + +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLN* 2.6 31.2 + - - +
103A VAL* 1.3 76.4 - - - +
105A ASP* 1.3 61.0 + - - +
106A CYS* 5.2 0.5 - - - +
115B SER* 3.0 37.3 - - - -
116B GLY* 3.7 22.6 - - - +
119B ASP* 2.8 33.6 + - - +
601B ASN* 3.6 16.7 + - - +
604B TYR* 3.4 42.7 - - + +
4E G 4.6 9.5 + - - -
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP* 2.7 43.6 + - + +
104A ARG* 1.3 77.3 - - - +
106A CYS* 1.3 71.3 + - - +
107A ARG* 3.0 32.8 + - + +
111B ALA 3.7 4.9 - - - +
114B GLY* 3.4 23.2 - - - -
115B SER* 3.5 6.4 + - - -
116B GLY 3.1 21.2 + - - -
117B PHE* 3.5 8.0 + - - +
4E G 5.4 5.8 - - - +
5E A 5.2 0.9 + - - -
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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
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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) + - + + + + + -
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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