Contacts of the strand formed by residues 122 - 133 (chain A) in PDB entry 3ECP
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 ARG 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A SER 3.6 0.3 - - - -
103A TYR* 2.7 34.8 + - - +
108A ALA 3.1 25.0 + - - +
109A GLU* 4.2 16.9 + - - +
111A LEU* 2.7 28.0 + - - -
112A GLY* 3.3 20.8 - - - +
113A LYS* 3.7 13.8 - - - +
114A LEU* 3.6 9.2 - - - +
116A SER 5.1 1.0 + - - -
117A ILE 4.2 12.7 + - - -
119A ASP 3.8 14.7 + - - +
120A LYS* 3.7 6.7 - - - +
121A SER* 1.3 81.2 - - - +
123A GLY* 1.3 60.7 + - - +
150A ARG 4.9 1.0 + - - -
152A ASP* 3.0 37.4 + - - +
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Residues in contact with GLY 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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101A LEU 3.2 9.6 - - - -
103A TYR* 4.4 0.4 - - - -
111A LEU* 3.5 24.3 - - - +
112A GLY* 3.0 34.0 + - - +
113A LYS 5.0 0.2 - - - +
114A LEU* 3.9 5.8 - - - +
122A ARG* 1.3 77.0 - - - +
124A TRP* 1.3 65.7 + - - -
125A TRP* 5.6 0.2 - - - -
149A MET* 4.6 2.8 - - - +
150A ARG 5.2 0.3 + - - -
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Residues in contact with TRP 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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100A SER* 3.4 3.6 - - - -
101A LEU* 2.8 38.9 + - + +
103A TYR* 4.0 17.0 - + - -
111A LEU* 3.9 24.2 - - + -
114A LEU* 3.7 4.7 - - - +
123A GLY* 1.3 78.3 - - - -
125A TRP* 1.3 67.0 + - - +
126A VAL* 4.5 4.5 - - + -
147A TRP* 3.8 38.7 - + + +
148A TRP* 3.6 16.4 - - - +
149A MET* 3.4 39.7 - - + +
346A PRO* 3.6 27.6 - - + -
349A LEU* 3.8 32.1 - - + -
350A GLU* 4.0 19.1 + - + -
353A VAL* 5.9 0.7 - - + -
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Residues in contact with TRP 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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98A THR* 3.9 13.5 - - + -
99A THR* 3.6 19.3 - - - -
100A SER* 3.6 22.9 - - - -
113A LYS 3.1 19.5 + - - -
114A LEU* 3.6 36.3 - - + +
123A GLY 5.6 0.4 - - - -
124A TRP* 1.3 74.2 - - - +
126A VAL* 1.3 60.7 + - - +
146A GLU 3.5 2.0 - - - +
147A TRP* 3.4 2.9 - - - -
148A TRP* 2.9 66.7 + + + -
150A ARG* 3.2 55.8 - - + +
161A GLU* 5.2 0.2 - - - -
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Residues in contact with VAL 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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97A ASP 4.0 1.0 - - - +
98A THR* 3.2 5.3 - - - -
99A THR* 2.9 35.9 + - + +
101A LEU* 3.5 34.5 - - + -
124A TRP* 4.5 1.6 - - + -
125A TRP* 1.3 79.6 - - - +
127A HIS* 1.3 62.6 + - - +
128A SER* 3.7 19.3 + - - +
145A GLN* 3.8 22.9 - - + +
146A GLU 3.1 7.6 - - - +
147A TRP* 3.8 24.2 - - + +
329A HIS* 5.0 0.9 + - - +
332A TRP* 3.8 11.9 - - + -
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Residues in contact with HIS 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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96A GLU* 2.6 45.2 + - + +
97A ASP* 3.4 13.3 - - - -
98A THR* 2.6 26.1 + - - +
125A TRP 4.2 0.4 - - - -
126A VAL* 1.3 72.1 - - - +
128A SER* 1.3 59.6 + - - +
144A HIS* 3.9 7.7 - + - -
145A GLN* 3.1 3.7 - - - -
146A GLU* 2.8 41.3 + - + +
148A TRP* 4.0 17.0 - - + -
164A LYS* 3.6 35.1 - - + +
165A TRP* 3.7 23.0 - + - -
168A ALA* 4.2 6.5 - - + -
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Residues in contact with SER 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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95A ILE 3.6 1.7 - - - +
96A GLU* 3.3 6.6 - - - +
97A ASP 2.9 34.2 + - - -
126A VAL* 3.7 5.9 - - - +
127A HIS* 1.3 73.8 - - - +
129A VAL* 1.3 65.6 + - - +
130A LEU 4.0 0.2 - - - -
142A LEU* 4.4 3.1 - - - -
144A HIS 3.3 4.5 - - - -
145A GLN* 2.7 36.3 + - - +
325A ILE* 4.2 10.0 - - - +
328A PHE* 3.9 15.7 - - - -
329A HIS* 4.4 5.4 + - - -
332A TRP* 4.7 0.3 - - - -
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Residues in contact with VAL 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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94A ALA* 3.8 31.2 - - + +
95A ILE 3.5 3.1 - - - +
96A GLU* 3.9 24.7 - - + +
128A SER* 1.3 77.4 - - - +
130A LEU* 1.3 62.8 + - - +
131A LEU* 4.7 0.4 - - + -
142A LEU* 3.6 6.8 - - - +
143A LEU* 2.9 43.1 + - + -
144A HIS* 2.8 44.0 + - + +
168A ALA* 4.1 3.8 - - + -
172A SER* 4.5 7.9 - - - +
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Residues in contact with LEU 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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93A LEU 3.5 1.6 - - - +
94A ALA* 4.5 0.9 - - - -
95A ILE* 2.8 42.9 + - + +
128A SER 4.0 0.8 - - - -
129A VAL* 1.3 72.1 - - - +
131A LEU* 1.3 62.4 + - - +
132A LEU* 3.7 24.2 + - + +
139A THR* 3.9 21.3 - - + +
141A GLY* 3.7 17.9 - - - +
142A LEU* 4.4 8.5 - - + -
324A ARG* 3.9 29.8 - - + +
325A ILE* 3.8 17.5 - - + -
328A PHE* 4.2 16.2 - - + -
361A VAL* 4.4 14.6 - - + -
364A LEU* 4.9 4.3 - - + -
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Residues in contact with LEU 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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82A THR* 3.8 20.9 - - + -
86A ALA* 4.0 14.6 - - + -
92A LEU* 4.0 18.4 - - + -
93A LEU 3.3 13.0 - - - +
94A ALA* 3.8 16.8 - - + -
129A VAL* 4.0 1.2 + - + -
130A LEU* 1.3 71.8 - - - +
132A LEU* 1.3 59.4 + - - +
139A THR* 3.9 1.0 - - - +
140A VAL* 2.8 34.7 + - + -
141A GLY 2.8 21.6 + - - +
143A LEU* 3.7 27.1 - - + -
176A MET* 3.9 26.7 - - + -
183A VAL* 4.7 6.5 - - + -
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Residues in contact with LEU 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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92A LEU* 3.2 11.9 - - - +
93A LEU* 2.8 42.5 + - + +
95A ILE* 3.7 29.4 - - + -
130A LEU* 3.8 24.5 - - + +
131A LEU* 1.3 82.4 - - - +
133A GLU* 1.3 68.1 + - - +
137A PHE* 4.0 11.4 - - + +
138A ARG 3.1 9.6 - - - +
139A THR* 3.8 11.0 - - - +
140A VAL* 3.8 0.7 - - - -
321A HIS* 4.8 4.0 - - + -
324A ARG* 3.5 39.9 - - + +
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Residues in contact with GLU 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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89A PHE* 3.5 53.0 - - + -
91A GLU 3.7 4.9 - - - +
92A LEU* 3.9 2.7 - - - -
93A LEU 4.9 0.2 - - - -
132A LEU* 1.3 74.8 - - - +
134A ALA* 1.3 57.7 + - - +
135A THR* 3.2 11.5 + - - +
136A THR* 2.3 45.6 + - - -
137A PHE* 2.9 30.9 + - - -
138A ARG* 2.8 43.5 + - + +
140A VAL* 3.5 4.3 - - + +
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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