Contacts of the helix formed by residues 119 - 135 (chain A) in PDB entry 2GC5
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 THR 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.8 1.8 - - - -
14A PRO 3.1 17.9 - - - +
15A ARG* 4.3 2.9 - - - -
16A LEU* 3.7 24.0 - - + +
24A ARG* 3.8 15.7 - - - +
118A VAL* 1.3 77.3 - - - +
120A GLU* 1.3 65.3 + - - +
121A PHE* 3.6 7.4 + - - +
122A GLU* 2.9 43.1 + - - +
123A PHE* 2.9 23.0 + - - +
152A SER* 4.8 0.5 + - - -
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Residues in contact with GLU 120 (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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10A ILE 3.2 21.5 - - - +
11A HIS* 2.8 45.8 + - - +
13A PHE* 3.4 23.2 - - + +
14A PRO 4.0 2.6 + - - -
82A ARG* 4.4 5.9 + - - -
119A THR* 1.3 73.7 - - - +
121A PHE* 1.3 63.7 + - - +
123A PHE* 3.3 3.4 + - - +
124A ILE* 3.0 47.8 + - + +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 3.4 22.2 - + - -
82A ARG* 5.3 9.6 - - - -
119A THR* 3.4 6.7 + - - +
120A GLU* 1.3 79.2 - - - +
122A GLU* 1.3 53.9 + - - +
124A ILE* 3.4 6.6 + - + -
125A THR* 2.8 49.9 + - - -
143A GLU 5.0 1.3 - - - -
145A GLY* 3.8 22.0 - - - -
151A ASP* 3.8 21.5 - - - -
152A SER* 3.3 28.9 - - - +
153A THR* 3.7 17.3 - - + -
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Residues in contact with GLU 122 (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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21A ASP 4.9 5.2 - - - +
22A HIS* 5.7 0.9 - - - -
24A ARG* 2.9 54.7 + - - +
25A ILE* 3.5 28.5 + - + +
28A LEU* 5.0 0.7 - - - -
118A VAL* 3.4 14.4 - - + +
119A THR* 2.9 39.5 + - - +
121A PHE* 1.3 73.9 - - - +
123A PHE* 1.3 64.3 + - - +
126A ALA* 3.0 25.6 + - - +
152A SER* 3.4 22.2 + - - +
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Residues in contact with PHE 123 (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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9A TYR* 3.7 22.2 - + - -
10A ILE* 3.8 30.7 - - + -
13A PHE* 3.4 36.3 - + + -
28A LEU* 4.4 6.1 - - + -
99A VAL* 4.0 13.0 - - + -
102A VAL* 3.4 39.3 - - + +
103A ARG* 4.0 6.3 - - - -
106A LEU* 4.8 3.8 - - + -
118A VAL* 3.9 14.7 - - + +
119A THR 2.9 19.7 + - - +
120A GLU 3.3 3.6 + - - +
122A GLU* 1.3 72.4 - - - +
124A ILE* 1.3 61.8 + - - +
126A ALA* 3.4 2.4 + - - +
127A LEU* 2.9 44.1 + - + +
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Residues in contact with ILE 124 (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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10A ILE* 3.5 25.8 - - + -
71A TYR* 3.3 27.6 + - + +
79A PHE* 3.7 28.5 - - + -
82A ARG* 3.5 30.3 - - - +
83A ILE* 4.3 10.8 - - + +
120A GLU* 3.0 35.2 + - + +
121A PHE* 3.9 5.8 - - + +
123A PHE* 1.3 77.1 - - + +
125A THR* 1.3 58.1 + - - +
127A LEU* 3.3 7.9 + - + +
128A GLY* 2.8 26.3 + - - -
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Residues in contact with THR 125 (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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25A ILE* 3.7 19.7 - - + -
71A TYR* 2.9 24.1 + - + -
121A PHE* 2.8 40.7 + - - -
124A ILE* 1.3 73.7 - - - +
126A ALA* 1.3 64.8 + - - +
128A GLY* 3.3 1.1 + - - +
129A TYR* 3.0 49.5 + - + -
152A SER* 4.0 9.4 - - - +
153A THR* 4.0 13.9 - - + -
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Residues in contact with ALA 126 (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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25A ILE* 4.0 8.2 - - + +
28A LEU* 3.6 26.5 - - + -
29A LEU* 3.8 29.1 - - + +
32A LEU* 4.1 9.4 - - + +
102A VAL* 5.0 0.2 - - + -
122A GLU 3.0 18.5 + - - +
123A PHE 3.8 1.6 - - - +
125A THR* 1.3 77.2 - - - +
127A LEU* 1.3 63.6 + - - +
129A TYR* 3.4 1.7 + - - +
130A TRP* 3.0 24.9 + - - +
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Residues in contact with LEU 127 (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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10A ILE* 5.2 2.0 - - + -
83A ILE* 3.8 22.0 - - + -
90A ILE* 4.5 2.9 - - + -
95A LEU* 4.3 11.4 - - + -
98A ALA* 3.8 22.2 - - + +
99A VAL* 3.7 45.1 - - + +
102A VAL* 4.0 18.1 - - + +
123A PHE* 2.9 28.0 + - + +
124A ILE* 3.4 7.2 - - - +
126A ALA* 1.3 76.3 - - - +
128A GLY* 1.3 53.4 - - - +
130A TRP* 3.3 4.1 + - + +
131A TYR* 2.8 43.3 + - + +
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Residues in contact with GLY 128 (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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71A TYR* 5.3 5.2 - - - -
83A ILE* 4.1 22.2 - - - -
124A ILE 2.8 19.2 + - - -
125A THR* 3.3 2.7 + - - -
126A ALA 3.3 0.2 - - - -
127A LEU* 1.3 74.6 - - - +
129A TYR* 1.3 61.9 + - - +
131A TYR* 3.3 4.6 + - - +
132A PHE* 2.9 39.3 + - - -
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Residues in contact with TYR 129 (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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29A LEU* 4.3 9.2 - - + -
35A PRO* 3.8 13.6 - - + -
36A GLN* 4.1 13.9 - - + +
41A TYR* 3.6 37.3 + + - -
71A TYR* 6.0 1.1 - + - -
125A THR* 3.0 44.2 + - + +
126A ALA 3.9 3.4 - - - +
128A GLY* 1.3 74.7 - - - +
130A TRP* 1.3 62.4 + - - +
132A PHE* 3.5 5.7 + + - +
133A ARG* 3.2 27.7 + - - +
142A ILE* 3.5 37.1 - - + +
153A THR 2.7 22.7 + - - -
155A VAL* 3.7 19.3 - - + -
156A ILE* 3.5 16.9 - - + +
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Residues in contact with TRP 130 (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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32A LEU* 3.6 39.2 + - + -
35A PRO* 3.6 16.1 - - + +
97A ASN 5.3 0.7 - - - -
98A ALA* 3.9 29.6 - - + -
101A PHE* 3.2 53.2 - + + -
102A VAL* 4.9 5.8 - - + -
126A ALA 3.0 17.9 + - - +
127A LEU* 3.6 7.2 - - - +
129A TYR* 1.3 75.8 - - - +
131A TYR* 1.3 71.0 + + + +
133A ARG* 3.1 4.7 + - + +
134A GLN* 2.8 67.7 + - + +
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Residues in contact with TYR 131 (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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83A ILE* 3.6 28.9 - - + -
85A ILE* 3.5 34.0 - - + +
88A GLU 5.6 0.7 + - - -
90A ILE* 3.6 40.5 - - + +
91A PRO* 3.7 14.7 - - - +
94A ALA* 4.3 11.1 - - + +
98A ALA* 5.1 6.7 - - + -
127A LEU* 2.8 27.8 + - + +
128A GLY* 3.7 4.3 - - - +
130A TRP* 1.3 84.0 - + + +
132A PHE* 1.3 65.7 + + - +
134A GLN* 3.1 19.2 + - - +
135A ARG* 3.0 44.1 + - + +
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Residues in contact with PHE 132 (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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41A TYR* 5.8 2.2 - - + -
69A GLY* 3.6 11.0 - - - -
70A LEU 3.6 26.7 - - - -
71A TYR* 3.9 20.9 - + + -
83A ILE* 3.8 22.7 - - + -
84A MET 3.5 20.4 - - - -
85A ILE* 4.2 11.2 - - + -
128A GLY* 2.9 26.8 + - - +
129A TYR* 3.8 9.0 - + - +
131A TYR* 1.3 77.6 - + - +
133A ARG* 1.3 63.0 + - - +
135A ARG* 3.5 1.3 + - - -
136A GLN 3.1 19.4 + - - -
137A VAL* 3.2 29.7 + - + +
140A ALA* 3.6 19.5 - - + -
142A ILE* 3.9 14.1 - - + -
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Residues in contact with ARG 133 (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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35A PRO* 3.1 39.7 - - + +
38A GLN* 3.6 13.1 - - - +
39A GLY* 3.7 22.6 - - - +
40A ARG 4.8 1.2 + - - +
41A TYR* 3.9 6.7 - - - -
129A TYR 3.2 11.5 + - - +
130A TRP* 3.1 8.7 + - + +
132A PHE* 1.3 84.2 + - - +
134A GLN* 1.3 67.3 + - - +
135A ARG 3.1 1.6 - - - -
136A GLN* 3.0 32.9 + - - +
137A VAL* 3.1 31.5 + - - +
901A SO4 2.8 50.4 + - - +
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Residues in contact with GLN 134 (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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130A TRP* 2.8 51.9 + - + +
131A TYR* 3.4 29.0 - - - +
133A ARG* 1.3 75.1 - - - +
135A ARG* 1.3 69.9 + - + +
136A GLN* 3.4 10.6 + - - +
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Residues in contact with ARG 135 (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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67A THR* 5.5 3.1 - - - +
85A ILE* 3.6 42.4 - - + +
131A TYR* 3.0 43.7 + - + +
132A PHE 4.1 2.0 - - - +
134A GLN* 1.3 85.2 - - - +
136A GLN* 1.3 74.3 + - - +
137A VAL* 3.3 3.8 + - + +
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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
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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