Contacts of the strand formed by residues 113 - 125 (chain A) in PDB entry 4KM9
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A THR* 3.1 29.3 + - + +
111A ASP 4.7 0.4 - - - +
112A GLY* 1.3 83.6 - - - +
114A SER* 1.3 60.2 + - - +
115A GLY 3.7 6.6 + - - +
116A PHE 4.9 0.9 - - - -
117A GLY* 3.8 20.9 - - - +
193A GLY* 4.1 1.3 - - - -
194A VAL* 3.9 11.2 - - + +
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Residues in contact with SER 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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96A SER* 3.5 11.3 - - - -
97A ASP* 3.3 29.0 + - - +
113A PRO* 1.3 69.6 - - - +
115A GLY* 1.3 61.3 + - - +
116A PHE 3.3 0.7 + - - -
117A GLY* 2.8 20.1 + - - -
190A THR* 3.5 12.6 + - - -
192A PHE* 3.4 18.7 - - - +
193A GLY* 3.6 16.6 - - - -
194A VAL 3.1 13.4 + - - +
195A VAL* 3.8 9.7 - - - +
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 3.8 15.9 - - - +
105A HIS* 3.4 29.8 - - - -
106A GLU 5.6 0.2 - - - -
108A THR* 4.2 12.6 - - - +
113A PRO* 3.7 12.0 + - - +
114A SER* 1.3 71.1 + - - +
116A PHE* 1.3 62.2 + - - -
117A GLY 3.2 0.7 + - - -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 2.9 26.9 + - + +
105A HIS* 3.5 27.8 - + - -
113A PRO* 4.9 2.2 - - - +
115A GLY* 1.3 73.5 - - - -
117A GLY* 1.3 54.9 + - - +
118A PHE* 3.2 32.9 - - + -
148A VAL* 3.5 37.5 - - + -
149A PHE* 3.9 24.0 - + - -
152A GLU* 3.8 38.6 - - + -
154A THR* 3.6 21.9 + - - -
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Residues in contact with GLY 117 (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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113A PRO* 3.8 22.0 - - - -
114A SER 2.8 17.0 + - - -
115A GLY 3.2 1.6 + - - -
116A PHE* 1.3 75.9 - - - +
118A PHE* 1.3 58.0 + - - +
194A VAL* 3.5 7.6 - - - +
195A VAL* 3.5 5.4 - - - -
196A THR* 3.0 28.7 + - - +
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Residues in contact with PHE 118 (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 LEU* 3.2 53.6 - - + +
96A SER* 3.6 0.5 + - - -
114A SER 4.4 0.6 + - - -
116A PHE* 3.2 35.0 - - + -
117A GLY* 1.3 79.9 - - - +
119A GLU* 1.3 75.5 + - - +
120A LEU* 3.9 15.7 - - + -
148A VAL* 4.4 12.6 - - + -
154A THR* 3.9 13.2 - - - -
155A PHE* 4.0 37.7 - + + -
195A VAL* 4.1 4.5 - - - +
196A THR* 3.3 23.8 - - - +
198A LEU* 3.7 26.2 - - + -
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Residues in contact with GLU 119 (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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37A ILE* 4.6 8.1 - - + -
91A ILE* 5.4 0.4 - - + -
92A SER* 2.6 50.4 + - - +
93A PHE* 3.4 2.2 + - - -
94A GLY 2.7 21.8 + - - -
95A LEU* 3.3 12.2 + - - +
96A SER* 2.6 41.4 + - - +
98A LEU* 4.2 1.8 - - - +
118A PHE* 1.3 79.2 - - - +
120A LEU* 1.3 64.0 + - - +
195A VAL* 4.1 7.0 - - + -
196A THR 3.2 5.7 + - - -
197A PHE* 3.6 23.7 - - + -
198A LEU 3.3 18.9 + - - -
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Residues in contact with LEU 120 (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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68A LEU* 5.3 1.1 - - + -
91A ILE* 4.4 0.2 - - - +
92A SER* 3.0 34.2 + - - +
95A LEU* 3.8 21.4 - - + +
118A PHE* 3.9 17.9 - - + -
119A GLU* 1.3 76.1 - - - +
121A THR* 1.3 64.1 + - - +
141A MET* 3.5 37.1 - - + +
144A LEU* 3.8 28.5 - - + -
145A ALA 4.8 1.1 - - - +
155A PHE* 5.5 0.4 - - + -
179A LEU* 4.0 17.5 - - + -
198A LEU* 3.5 12.8 - - + +
200A ILE* 4.0 22.9 - - + -
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Residues in contact with THR 121 (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 HIS* 3.7 5.2 - - - +
90A TYR 3.0 11.4 - - - -
91A ILE* 3.7 20.6 - - + -
120A LEU* 1.3 79.3 - - - +
122A PHE* 1.3 64.8 + - - +
141A MET* 4.4 2.2 - - - -
182A ASP* 2.6 29.5 + - - +
185A MET* 4.3 3.6 - - + -
197A PHE* 4.2 27.1 - - + -
198A LEU 3.0 5.1 + - - +
199A GLN* 3.3 16.5 + - - +
200A ILE* 2.9 29.5 + - - +
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Residues in contact with PHE 122 (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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88A TRP 3.5 1.2 - - - +
89A HIS* 3.5 6.1 - - - -
90A TYR* 2.9 45.9 + + + -
121A THR* 1.3 80.0 + - - +
123A ARG* 1.3 67.8 + - - +
124A LEU* 3.6 42.4 - - + -
136A TRP* 4.2 9.6 - + - -
137A PRO* 3.7 32.1 - - + -
141A MET* 4.8 5.4 - - + -
167A LEU* 5.5 5.6 - - + -
199A GLN* 4.2 5.6 - - - -
200A ILE* 3.5 36.1 - - + -
202A GLY 4.9 1.3 - - - -
236A THR* 3.6 29.6 - - + -
238A MET* 5.5 0.2 - - - -
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Residues in contact with ARG 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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76A ASN* 3.9 1.2 + - - -
87A HIS* 3.0 41.5 + - + -
88A TRP 3.3 4.0 - - - -
89A HIS* 3.2 31.5 + - + -
122A PHE* 1.3 85.2 - - - +
124A LEU* 1.3 56.0 + - - +
182A ASP* 2.8 30.7 + - - -
183A PRO* 3.9 11.0 - - - +
184A GLN* 3.5 28.7 + - - +
199A GLN* 3.6 27.5 + - + +
233A TRP* 3.7 28.5 - - - -
234A LEU 4.5 0.3 - - - +
235A ILE* 4.0 12.6 - - + -
236A THR* 2.8 36.6 + - - -
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Residues in contact with LEU 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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87A HIS* 3.2 2.6 - - - +
88A TRP* 2.7 49.1 + - + +
90A TYR* 4.3 9.0 - - + +
122A PHE* 3.6 25.0 - - + -
123A ARG* 1.3 72.1 - - - +
125A LYS* 1.3 70.1 + - - +
130A GLU* 4.7 4.0 - - - +
134A PRO* 3.6 30.3 - - + -
136A TRP* 3.6 32.5 - - + +
137A PRO* 4.4 1.8 - - + -
236A THR 3.5 9.9 - - - +
238A MET* 3.7 20.4 - - + +
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Residues in contact with LYS 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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85A PRO* 3.9 26.5 - - + -
86A GLU 3.8 11.2 - - - +
87A HIS* 3.8 0.2 - - - -
88A TRP* 4.5 0.9 - - - -
124A LEU* 1.3 82.0 - - - +
126A ARG* 1.3 78.7 + - - +
127A GLU* 3.5 8.1 + - - +
130A GLU* 4.1 4.3 - - - +
228A ILE 5.9 1.6 - - - +
235A ILE* 3.4 15.4 - - + +
236A THR 2.9 18.3 + - - +
237A ASP* 3.5 39.3 + - + +
239A ARG* 6.0 1.0 - - - +
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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