Contacts of the strand formed by residues 99 - 113 (chain A) in PDB entry 4STD
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 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 2.8 41.6 + - + +
96A SER* 2.8 37.6 + - - +
97A GLU 3.7 0.2 - - - -
98A ASP* 1.3 93.2 - - - +
100A VAL* 1.3 65.0 + - - +
135A TYR 3.4 7.0 - - - +
136A LYS* 3.6 25.5 + - + +
142A TRP* 4.1 0.2 - - - -
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.7 26.0 - - + -
19A LEU* 3.9 26.5 - - + -
92A TRP* 3.9 10.1 - - + -
93A GLU 3.3 13.7 - - - +
94A LYS* 4.0 10.1 - - + -
95A VAL* 4.1 0.7 - - - +
96A SER 5.1 0.2 - - - +
99A GLU* 1.3 78.5 - - - +
101A ILE* 1.3 76.3 + - - +
134A TRP* 3.8 2.3 - - - -
135A TYR* 2.8 34.5 + - + +
142A TRP* 3.4 30.7 - - + -
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG 4.0 0.2 - - - +
92A TRP* 3.6 1.4 - - - -
93A GLU* 2.7 49.9 + - + +
95A VAL* 3.6 21.3 - - + -
100A VAL* 1.3 83.0 - - - +
102A GLY* 1.3 61.9 + - - +
103A TYR* 3.6 30.3 - - + +
132A LEU* 3.3 26.9 - - + -
133A HIS 3.3 2.5 - - - -
134A TRP* 3.8 33.7 - - + +
135A TYR* 4.5 0.2 - - - -
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG 3.4 4.9 - - - -
92A TRP* 3.5 21.8 - - - -
101A ILE* 1.3 75.1 - - - +
103A TYR* 1.3 63.2 + - - -
104A HIS* 3.7 12.3 - - - -
131A ASN 3.4 2.8 - - - +
132A LEU* 3.6 2.3 - - - -
133A HIS 2.9 35.3 + - - -
135A TYR* 3.9 2.6 - - - -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.1 6.9 - - - -
91A ARG* 2.7 81.2 + - + +
93A GLU* 3.4 34.0 + - + -
101A ILE* 3.6 20.3 - - + +
102A GLY* 1.3 71.2 - - - -
104A HIS* 1.3 61.7 + - - +
130A ALA 6.5 0.2 - - - -
131A ASN 3.4 2.9 - - - -
132A LEU* 3.8 32.9 - - + +
24B TYR* 3.4 30.9 - + + +
37B ARG* 6.2 0.4 - - - -
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.9 14.3 - - + +
87A ILE* 4.3 10.5 - - + +
89A GLY 3.6 2.7 - - - -
90A THR* 3.0 40.9 + - + +
92A TRP* 3.5 20.2 - + - -
102A GLY* 3.7 16.7 + - - -
103A TYR* 1.3 72.5 - - - +
105A GLN* 1.3 69.1 + - - +
106A LEU* 4.5 6.1 - - + -
130A ALA 3.8 0.2 - - - -
131A ASN* 2.8 47.1 + - + +
133A HIS* 3.3 33.2 - + - -
135A TYR* 2.9 19.7 + - - -
24B TYR* 4.2 4.0 + - - -
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Residues in contact with GLN 105 (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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87A ILE* 3.7 0.5 - - - -
88A GLY 2.9 23.6 + - - -
89A GLY* 2.8 45.6 + - - +
104A HIS* 1.3 72.9 - - - +
106A LEU* 1.3 63.8 + - - +
129A SER 3.7 5.2 - - - -
130A ALA* 4.9 2.0 - - - +
24B TYR* 3.7 15.4 - - + -
27B ALA* 3.7 16.2 - - - +
28B ASP* 4.7 8.9 + - + +
31B ASP* 4.2 9.1 + - - -
84B GLN* 4.9 3.4 - - - +
85B HIS 3.1 25.4 + - - -
86B PHE* 3.4 19.3 - - + +
87B ILE* 3.0 24.6 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 3.9 23.1 - - + -
85A HIS* 4.5 5.4 - - + +
86A PHE 3.4 17.3 - - - +
87A ILE* 4.0 20.0 - - + -
104A HIS* 4.5 11.2 - - + -
105A GLN* 1.3 79.7 - - - +
107A ARG* 1.3 60.5 + - - +
108A VAL* 3.7 15.9 - - + -
127A ALA 3.7 0.2 - - - +
129A SER* 2.7 52.2 + - - +
131A ASN* 3.4 26.9 - - - +
173A BFS 3.5 20.9 - - + -
84B GLN* 3.0 8.4 + - - +
86B PHE* 3.7 0.6 - - - -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 3.2 12.8 + - - +
86A PHE* 3.2 27.4 + - + +
106A LEU* 1.3 72.0 - - - +
108A VAL* 1.3 61.4 + - - +
109A PRO* 3.6 28.3 - - - +
126A HIS* 3.2 36.3 + - - +
127A ALA 3.2 3.6 - - - +
128A HIS* 3.5 18.5 + - + -
155A GLU* 3.9 8.9 + - - -
84B GLN* 3.2 24.5 - - - +
86B PHE* 3.8 19.2 - - + -
107B ARG* 3.9 21.6 - - - +
107C ARG* 3.1 47.4 - - - +
128C HIS* 4.5 0.6 + - - -
155C GLU* 4.2 2.0 + - - -
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 4.4 0.7 - - - -
84A GLN 3.2 14.1 - - - +
85A HIS* 3.6 31.9 - - + +
106A LEU* 3.7 19.7 - - + -
107A ARG* 1.3 80.1 - - - +
109A PRO* 1.3 62.8 - - - +
110A HIS* 3.1 30.3 + - + +
126A HIS* 3.2 1.1 - - - -
127A ALA 2.8 33.1 + - - +
173A BFS 3.7 33.2 - - + -
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Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 3.1 23.6 - - - -
84A GLN* 3.2 26.3 + - + +
107A ARG* 3.6 31.0 - - - +
108A VAL* 1.3 85.9 - - - +
110A HIS* 1.3 58.6 + - - +
126A HIS* 3.0 34.5 - - + +
128C HIS* 3.9 18.8 - - + +
153C TRP* 3.8 10.7 - - + -
155C GLU* 5.0 0.9 - - - +
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Residues in contact with HIS 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.2 4.0 - - + -
82A ARG 3.4 4.7 - - - -
83A THR* 3.3 23.0 - - + +
85A HIS* 4.8 3.2 + - - -
108A VAL* 3.1 37.8 + - + +
109A PRO* 1.3 71.5 - - - +
111A GLN* 1.3 61.5 + - - +
112A ARG 4.3 0.4 - - - -
123A MET 4.5 0.2 - - - -
124A LYS* 3.3 5.8 - - - -
125A GLY 2.8 49.2 + - - +
126A HIS* 3.3 5.9 + - - -
158A PHE* 3.3 23.3 - + - -
161A ILE* 3.8 24.7 - - + -
162A PHE* 3.5 31.9 - + - -
173A BFS 3.5 10.2 - - - -
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Residues in contact with GLN 111 (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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80A THR 3.7 1.4 - - - +
81A LEU* 3.6 2.7 - - - +
82A ARG* 2.8 37.5 + - + +
110A HIS* 1.3 75.6 - - - +
112A ARG* 1.3 60.9 + - - +
113A TYR* 2.6 36.2 + - + -
121A VAL* 3.8 30.1 - - + +
123A MET 3.4 2.9 - - - -
124A LYS* 3.4 22.8 - - + +
126A HIS* 5.5 0.2 - - + -
153C TRP* 3.2 24.2 - - + -
154C GLY 3.0 18.4 + - - -
155C GLU* 3.6 18.4 - - - +
156C PHE 4.4 2.3 + - - -
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Residues in contact with ARG 112 (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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74A GLN 5.7 1.0 + - - -
75A VAL 5.4 0.8 + - - -
78A ASP* 2.6 33.7 + - - +
80A THR* 3.2 11.7 - - - +
81A LEU* 3.8 24.0 - - + +
110A HIS 4.3 0.2 - - - -
111A GLN* 1.3 74.1 - - - +
113A TYR* 1.3 66.6 + - - +
121A VAL* 3.6 4.2 - - - +
122A THR* 2.7 34.6 + - - -
123A MET* 2.8 54.9 + - + +
161A ILE* 2.7 42.0 + - + +
162A PHE* 4.9 3.2 - - - -
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Residues in contact with TYR 113 (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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80A THR* 2.8 33.0 + - - +
82A ARG* 3.5 16.4 - - + -
111A GLN* 2.6 32.4 + - + -
112A ARG* 1.3 79.5 - - - +
114A LYS* 1.3 64.4 + - - +
115A ASP 3.5 16.4 - - - +
118A MET* 3.4 60.3 - - + -
119A LYS 5.7 0.2 - - - -
120A GLU 3.2 20.4 - - - +
121A VAL* 3.5 24.7 - - + -
122A THR* 3.2 9.0 + - - -
153C TRP* 4.0 12.5 - - - +
154C GLY 3.8 6.2 + - - -
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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