Contacts of the strand formed by residues 102 - 110 (chain H) in PDB entry 6D48
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 GLY 102 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100H ASP 3.4 1.0 + - - -
101H ASN* 1.3 74.2 - - - +
103H SER* 1.3 62.3 + - - -
104H TYR* 3.5 11.6 - - - -
123H SER* 4.4 1.3 - - - -
124H VAL 2.7 33.8 + - - -
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Residues in contact with SER 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ARG* 3.8 3.6 - - - +
51H GLU* 3.0 48.1 + - - +
102H GLY* 1.3 72.9 - - - -
104H TYR* 1.3 69.5 + - - +
121H GLN* 3.7 15.4 - - - +
122H LEU 3.1 6.7 - - - -
123H SER* 3.1 20.8 + - - -
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Residues in contact with TYR 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H TRP* 3.8 21.6 - - + -
49H PHE 3.1 19.5 - - - +
50H ARG* 3.9 33.9 + - + -
51H GLU 4.3 0.7 - - - +
61H VAL* 4.1 17.7 - - + -
74H THR* 4.9 0.5 - - - +
78H PHE* 3.7 27.9 - + - -
91H LEU* 5.4 3.4 - - + -
99H ARG 4.8 0.5 + - - -
100H ASP* 2.6 32.5 + - - -
101H ASN 4.5 1.6 + - - -
102H GLY* 3.5 20.2 - - - -
103H SER* 1.3 79.3 - - - +
105H PHE* 1.3 60.1 + - - +
121H GLN* 3.4 9.7 - - - +
122H LEU* 2.9 42.9 + - + +
124H VAL* 3.7 18.6 - - + -
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Residues in contact with PHE 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H TYR 3.8 0.2 - - - +
48H TRP* 3.4 9.2 - - - -
49H PHE* 2.8 63.8 + + + -
50H ARG 3.4 24.2 - - - -
51H GLU* 4.2 6.5 - - - -
52H GLY 4.6 2.2 - - - -
53H ALA* 4.2 20.9 - - + -
55H ILE* 4.4 6.7 - - + -
104H TYR* 1.3 75.3 - - - +
106H PHE* 1.3 69.5 + - - +
107H ARG* 4.7 0.9 - - + -
116H SER* 3.9 25.1 - - - -
117H TYR 3.8 18.2 - - - +
118H LYS* 6.1 0.2 - - - -
120H PRO 5.4 1.3 - - - +
121H GLN* 3.8 27.6 - - + +
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Residues in contact with PHE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H LEU* 4.1 20.0 - - + +
31H PHE* 3.6 34.8 - + - -
46H GLY* 3.8 14.1 - - - -
47H TYR 3.3 31.2 - - - -
48H TRP* 3.6 38.7 - + + -
80H LEU* 4.5 4.0 - - + -
84H PRO* 5.2 2.2 - - + -
89H CYS* 3.5 28.7 - - + -
105H PHE* 1.3 76.7 - - - +
107H ARG* 1.3 76.0 + - - +
108H MET* 4.1 6.3 - - + -
116H SER* 3.8 0.9 - - - -
117H TYR* 3.0 43.8 + + - +
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Residues in contact with ARG 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H GLY* 3.5 3.6 - - - -
47H TYR* 2.9 46.1 + - + +
49H PHE* 4.1 22.9 - - + -
55H ILE* 3.4 34.4 - - - +
105H PHE* 4.7 0.4 - - + -
106H PHE* 1.3 80.8 - - - +
108H MET* 1.3 67.5 + - - +
109H GLU* 2.9 28.8 + - + -
114H LYS* 3.6 28.2 - - - +
115H TYR* 3.3 14.9 - - - +
116H SER* 2.9 37.6 + - - +
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Residues in contact with MET 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H PHE* 4.0 33.7 - - + -
33H HIS* 4.2 13.5 - - + +
35H ILE* 3.9 26.5 - - + -
44H VAL* 5.0 4.7 - - + -
45H HIS 3.4 6.7 - - - +
106H PHE* 4.1 8.2 - - + -
107H ARG* 1.3 73.7 - - - +
109H GLU* 1.3 67.4 + - - +
110H ARG* 4.3 13.5 - - + +
113H THR* 3.9 23.8 - - - +
115H TYR* 2.9 47.4 + - + +
117H TYR* 4.3 16.6 - - + +
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H PRO 3.7 2.5 - - - +
44H VAL* 3.7 1.0 - - - +
45H HIS* 2.9 41.1 + - + +
47H TYR* 3.4 34.6 + - + -
55H ILE* 4.8 2.9 - - - +
107H ARG* 2.9 32.1 + - - +
108H MET* 1.3 81.7 - - - +
110H ARG* 1.3 62.0 + - - +
111H GLY 4.2 1.1 - - - +
113H THR 3.4 4.3 - - - -
114H LYS* 3.7 31.0 - - + +
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Residues in contact with ARG 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PRO* 3.9 23.6 + - - +
35H ILE* 3.8 36.0 - - + +
39H ASP* 3.3 31.8 + - + +
40H LYS* 2.9 27.7 + - - +
42H SER* 3.8 15.0 + - - +
43H PRO 3.8 4.0 - - - +
44H VAL* 3.7 29.1 - - + +
84H PRO 5.8 0.2 + - - -
85H SER 5.4 4.4 + - - -
87H ASN* 5.2 7.3 + - - -
108H MET* 4.3 13.2 - - + -
109H GLU* 1.3 75.1 - - - +
111H GLY* 1.3 67.2 + - - +
112H SER 3.1 0.9 + - - -
113H THR* 2.7 26.1 + - - +
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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