Contacts of the strand formed by residues 123 - 131 (chain A) in PDB entry 6S1M
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 PRO 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A HIS* 3.7 26.5 - - + +
104A TYR 3.4 7.4 - - - +
105A VAL* 4.5 3.6 - - + -
121A SER* 3.9 8.7 - - - +
122A VAL* 1.3 90.9 - - + +
124A VAL* 1.3 61.1 + - - +
125A LEU* 4.6 5.2 - - - +
143A GLY 4.9 1.9 + - - -
144A PHE 3.6 30.7 + - - +
146A PRO* 4.9 0.4 - - + -
215A ALA 3.9 22.4 - - - +
216A LEU* 4.0 9.4 - - + -
217A PRO* 4.1 10.8 - - + -
250A PHE* 4.3 7.6 - - + -
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Residues in contact with VAL 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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103A HIS* 4.3 0.9 + - - -
104A TYR* 2.7 69.2 + - + +
106A GLY* 4.7 7.2 - - - +
107A PRO 5.9 2.9 - - - +
109A GLN* 6.5 0.2 - - + -
121A SER 4.0 15.3 - - - +
122A VAL 3.3 6.0 + - - +
123A PRO* 1.3 78.4 - - - +
125A LEU* 1.3 62.0 + - - +
126A ARG* 6.0 0.2 - - + -
140A HIS* 5.1 7.9 - - - +
141A ILE 3.5 11.9 - - - +
142A HIS* 3.4 36.3 - - + +
143A GLY 5.2 0.2 - - - +
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Residues in contact with LEU 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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101A ILE* 5.9 6.3 - - + -
102A ASP 3.5 12.8 - - - +
103A HIS* 5.3 1.3 - - - +
123A PRO 4.6 5.8 - - - +
124A VAL* 1.3 78.5 - - - +
126A ARG* 1.3 66.0 + - - +
139A CYS 3.6 0.7 - - - +
140A HIS* 3.5 6.1 + - - +
141A ILE* 2.9 48.3 + - + +
144A PHE* 4.9 7.4 - - + -
250A PHE* 3.9 34.8 - - + -
251A GLU* 5.4 10.3 - - + -
254A PHE* 3.6 52.0 - - + -
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Residues in contact with ARG 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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101A ILE* 3.4 7.0 - - - +
102A ASP* 2.7 67.9 + - + +
103A HIS 4.2 5.1 + - - -
104A TYR* 3.9 44.5 - - + +
124A VAL* 6.0 0.2 - - + -
125A LEU* 1.3 81.3 - - - +
127A ALA* 1.3 62.0 + - - +
128A PHE* 3.9 24.2 - - + -
138A CYS* 5.0 3.4 - - - -
139A CYS 3.5 4.5 - - - +
140A HIS* 4.2 26.0 - - + +
141A ILE* 5.7 0.2 - - - -
282A THR* 5.2 2.5 - - - -
424A VAL* 3.8 31.1 - - - +
427A LEU* 5.2 6.9 - - - +
452A VAL* 5.2 7.2 - - - +
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Residues in contact with ALA 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 PHE* 4.4 10.0 - - + -
98A GLN* 4.8 9.4 - - + +
100A GLU 3.6 6.7 - - - +
101A ILE* 4.8 8.5 - - + -
126A ARG* 1.3 75.4 - - - +
128A PHE* 1.3 63.6 + - - +
137A VAL 3.7 1.0 - - - +
138A CYS* 3.6 2.1 - - - -
139A CYS* 2.9 49.6 + - + +
141A ILE* 4.8 13.7 - - + -
266A LEU* 5.3 5.8 - - + -
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Residues in contact with PHE 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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96A PHE* 4.4 1.6 - - - -
98A GLN* 3.3 6.3 - - - +
99A LEU* 2.8 26.3 + - + -
100A GLU* 3.0 29.8 + - + +
102A ASP* 4.1 14.1 - - + -
126A ARG* 3.9 37.7 - - + -
127A ALA* 1.3 74.1 - - - +
129A GLY* 1.3 59.6 + - - +
137A VAL 3.5 3.8 - - - +
138A CYS* 4.0 28.3 - - + -
282A THR* 5.2 5.6 - - + -
284A CYS* 4.7 5.4 - - - -
423A ARG* 4.0 33.9 - - + +
424A VAL* 5.2 6.1 - - + -
452A VAL* 5.0 3.6 - - + -
453A GLY* 3.9 34.1 - - - +
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Residues in contact with GLY 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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96A PHE* 3.7 13.4 - - - -
97A GLN 3.1 13.5 - - - -
98A GLN* 3.9 0.4 - - - -
99A LEU* 4.2 6.1 - - - -
128A PHE* 1.3 76.0 - - - +
130A VAL* 1.3 68.3 + - - +
136A SER* 3.7 2.6 - - - -
137A VAL 2.9 31.7 + - - -
423A ARG* 5.4 3.5 + - - +
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Residues in contact with VAL 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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81A ARG* 3.9 21.3 - - - +
96A PHE* 3.9 4.9 - - - -
97A GLN* 2.9 35.1 + - + +
99A LEU* 5.2 2.7 - - + -
129A GLY* 1.3 79.5 - - - +
131A THR* 1.3 65.9 + - - +
134A GLY* 5.4 2.9 - - - -
135A PHE 3.4 12.8 - - - +
136A SER* 4.6 2.5 - - - -
137A VAL* 4.9 0.4 - - - +
265A TRP* 4.4 0.2 - - - -
308A ALA* 3.8 24.4 - - + +
309A PRO* 5.5 6.5 - - + +
310A LEU* 3.8 18.8 - - + -
391A ASP* 3.7 22.2 - - - +
423A ARG* 5.7 1.8 - - - +
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Residues in contact with THR 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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94A LEU* 5.0 6.1 - - + -
95A ILE 4.1 15.7 - - - +
96A PHE* 4.1 2.7 - - + -
130A VAL* 1.3 79.0 - - - +
132A ASP* 1.3 60.5 + - - +
133A GLU* 3.1 6.8 + - - -
134A GLY* 3.1 9.5 + - - -
135A PHE* 2.9 48.4 + - + +
137A VAL* 3.7 25.6 - - + -
265A TRP* 4.8 2.9 - - - -
286A LEU* 4.3 7.2 - - + -
308A ALA* 4.0 13.2 - - - +
309A PRO* 4.6 1.7 - - - +
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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