Contacts of the strand formed by residues 99 - 115 (chain A) in PDB entry 4N1D
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 VAL 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.5 8.7 - - + -
91A LEU* 3.7 31.9 - - + -
92A TYR 3.5 7.2 - - - +
93A LEU* 3.9 18.2 - - + -
97A GLU 3.8 2.0 + - - +
98A LYS* 1.3 74.2 - - - +
100A VAL* 1.3 62.8 + - - +
101A LEU 4.4 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
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90A MET 3.6 1.4 - - - +
91A LEU* 3.4 7.5 - - - +
92A TYR* 2.7 70.8 + - + +
94A ASP* 4.1 24.5 - - + +
98A LYS* 3.7 13.7 - - + +
99A VAL* 1.3 78.6 - - - +
101A LEU* 1.3 70.4 + - - +
102A LYS* 4.1 5.8 - - + -
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Residues in contact with LEU 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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89A SER* 4.4 17.9 - - - -
90A MET 3.5 20.0 - - - +
91A LEU* 4.0 20.0 - - + +
100A VAL* 1.3 77.3 - - - +
102A LYS* 1.3 63.0 + - - +
103A ASN* 5.9 0.7 - - - +
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Residues in contact with LYS 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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89A SER* 3.4 1.5 - - - -
90A MET 2.8 36.4 + - - +
92A TYR* 4.1 19.3 - - + +
100A VAL* 4.4 4.9 - - + -
101A LEU* 1.3 79.3 - - - +
103A ASN* 1.3 82.5 + - - +
104A TYR* 3.5 47.8 + - + +
105A GLN* 5.3 1.2 - - - +
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Residues in contact with ASN 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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87A ALA* 4.8 6.5 - - + -
88A ILE 3.6 4.7 - - - +
89A SER* 2.6 31.4 + - - -
101A LEU* 5.9 0.9 - - - +
102A LYS* 1.3 88.8 + - - +
104A TYR* 1.3 61.4 + - - +
105A GLN* 3.7 19.8 + - - +
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Residues in contact with TYR 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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31A TRP* 4.2 11.3 - + - -
87A ALA* 3.1 24.1 - - - -
88A ILE* 2.8 16.5 + - + +
90A MET* 3.6 43.5 - - + -
92A TYR* 3.2 34.1 + + - -
102A LYS* 3.6 44.7 - - + +
103A ASN* 1.3 70.8 - - - +
105A GLN* 1.3 59.9 + - - +
107A MET* 3.2 28.7 - - + +
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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 ALA* 3.8 21.5 + - - +
102A LYS* 5.3 1.0 - - - +
103A ASN* 3.7 22.1 + - - +
104A TYR* 1.3 75.8 - - - +
106A ASP* 1.3 82.7 + - - +
107A MET* 3.2 8.1 + - - +
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Residues in contact with ASP 106 (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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85A LEU* 3.7 49.2 - - + +
86A SER 3.7 8.5 + - - +
105A GLN* 1.3 84.3 + - - +
107A MET* 1.3 62.9 + - - +
108A VAL 3.7 1.3 - - - -
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Residues in contact with MET 107 (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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23A PHE* 4.4 4.7 - - + -
38A TYR* 2.9 45.4 + - + +
40A ALA* 3.6 8.3 - - - +
85A LEU* 5.1 1.3 - - - -
86A SER 2.9 7.0 + - - +
88A ILE* 3.9 37.0 - - + +
90A MET* 4.0 23.6 - - + -
104A TYR* 3.2 39.3 - - + +
105A GLN 3.4 7.4 - - - +
106A ASP* 1.3 78.8 - - - +
108A VAL* 1.3 60.4 + - - +
109A VAL 4.3 0.2 - - - -
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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
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38A TYR* 3.8 11.2 - - + -
39A ASN 3.9 6.7 - - - +
40A ALA 3.5 3.1 - - - -
41A TYR* 3.7 24.0 - - + -
85A LEU* 3.1 6.7 - - - -
86A SER* 2.9 42.1 + - - +
87A ALA 4.8 0.2 - - - +
88A ILE* 3.5 28.9 - - + -
106A ASP 3.7 0.2 - - - -
107A MET* 1.3 84.8 - - - +
109A VAL* 1.3 75.0 + - - +
110A GLU* 3.8 15.0 - - - +
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Residues in contact with VAL 109 (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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16A ARG* 2.7 41.1 + - + -
40A ALA 2.9 18.6 + - - +
41A TYR* 3.7 20.5 - - + +
42A ARG* 4.2 4.9 - - - -
43A CYS* 3.6 18.2 - - - -
82A PRO* 3.6 27.6 - - + -
84A GLU 3.9 3.4 - - - -
85A LEU* 4.0 8.7 - - + -
107A MET 6.1 0.2 - - - -
108A VAL* 1.3 75.4 - - - +
110A GLU* 1.3 54.4 + - - +
111A GLY 3.6 22.9 - - - +
112A CYS* 3.9 5.2 - - - -
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Residues in contact with GLU 110 (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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16A ARG* 3.0 37.7 + - - +
84A GLU* 2.8 20.5 + - + +
85A LEU 4.3 1.1 - - - -
86A SER* 2.9 39.5 + - - +
108A VAL* 3.4 9.2 + - - +
109A VAL* 1.3 75.3 - - - +
111A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 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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16A ARG* 5.7 1.8 - - - -
82A PRO* 3.4 6.8 - - - +
83A THR* 2.8 27.7 + - - -
84A GLU* 3.2 23.2 + - - +
109A VAL* 3.6 4.3 - - - +
110A GLU* 1.3 80.8 - - - +
112A CYS* 1.3 64.1 + - - -
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Residues in contact with CYS 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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14A CYS* 4.2 9.6 - - - -
15A LYS* 4.1 12.8 - - - -
16A ARG* 3.5 29.1 - - + +
43A CYS* 2.0 54.3 - - + -
54A GLU 5.5 0.2 - - - +
55A PHE* 5.0 1.4 - - - -
56A HIS* 4.2 15.1 + - - -
81A VAL 3.4 5.4 - - - -
83A THR* 3.5 8.8 + - - -
109A VAL* 3.9 3.1 - - - -
111A GLY* 1.3 74.1 - - - -
113A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A CYS* 3.9 6.5 - - - -
55A PHE* 3.2 16.2 - - - -
56A HIS* 5.1 1.1 - - - -
79A CYS 3.3 1.4 - - - +
80A CYS* 3.4 2.1 - - - -
81A VAL* 2.9 34.7 + - - +
83A THR* 3.5 13.2 - - - +
112A CYS* 1.3 76.6 - - - +
114A CYS* 1.3 65.2 + - - -
115A ARG* 3.9 3.1 + - - -
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Residues in contact with CYS 114 (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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14A CYS* 3.9 11.7 - - - -
47A CYS* 2.0 50.9 - - + -
51A VAL* 3.9 17.9 - - + -
55A PHE* 3.0 27.5 + - - -
57A PRO* 3.4 13.5 - - - +
61A ALA* 3.6 5.2 - - - +
78A THR* 3.5 12.1 - - - +
79A CYS 3.4 4.0 - - - -
113A GLY* 1.3 72.5 - - - -
115A ARG* 1.3 73.8 + - - +
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Residues in contact with ARG 115 (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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55A PHE 3.9 0.6 + - - -
56A HIS* 2.3 38.0 + - - +
57A PRO* 3.6 1.4 - - - +
58A THR* 3.7 32.1 + - - +
60A HIS* 4.9 6.6 + - - -
61A ALA* 3.8 21.6 + - - +
64A GLN* 5.3 3.6 + - - +
78A THR* 3.4 8.7 - - - +
79A CYS* 2.9 32.3 + - + +
81A VAL* 3.7 27.8 - - + -
83A THR* 3.4 34.4 + - + +
113A GLY* 4.2 0.4 - - - -
114A CYS* 1.3 92.9 + - - +
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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
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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